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		<title>SME: Simple Molecule Editor</title>
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				<h3> <b>SME</b> - Simple Molecule Editor</h3>
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			<a name="intro"></a>
			<h1> Introduction </h1>
				<p>
					SME is the Simple Molecule Editor originally designed for use with <a href="http://code.google.com/p/origindb/"> OriginDB</a>. SME provides users with a very simplified interface for creating and editing the 2D structure of molecules. The features of SME are meant to be as few as possible to increase the simplicity of the application. If you need a more feature rich application for molecular editing see <a href="http://avogadro.openmolecules.net/"> Avogadro </a> or <a href="http://molsketch.sourceforge.net/"> MolSketch </a> or many proprietary applications.
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			<a name="editing"></a>
			<h1> Editing </h1>
				<p>
					This is an intro into editing
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			<a name="tools"></a>
			<h2> Tools </h2>
				<p>
					SME provides you with many tools to create molecules. Below is an explination of each of them.
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				<ul class="images">
					<li>
						<a name="draw"></a>
						<img class="inline" src="images/draw-freehand.png"/>
						<p>
							This is the draw tool. While this tool is selected you can add atom by clicking on the position you want to add the atom. You can also add bonds by clicking on the atom and dragging.
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					<li>
						<a name="erase"></a>
						<img class="inline" src="images/draw-eraser.png"/>
						<p>
							This is the erase tool. While this tool is selected you can erase atom by clicking on the atom you want to erase. You can also erase bonds by clicking on the bond you want to erase. Note that if you erase and atom that has bonds attached to it the bonds will also be erased.
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					<li>
						<a name="move"></a>
						<img class="inline" src="images/transform-move.png"/>
						<p>
							This is the move tool. Click and drag on the item you want to move. If you want to move multiple items, hold <i>Ctrl</i> while selecting the items you want to move, and then click and drag the items.
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					<li>
						<a name="rotate"></a>
						<img class="inline" src="images/transform-rotate.png"/>
						<p>
							This is the rotate tool. This tool is used for rotating the entire molecule. First select the molecule, and then you can rotate it. Note that this feature currently sometimes does not behave correctly.
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					<li>
						<a name="flip"></a>
						<img class="inline" src="images/object-flip-horizontal.png"/>
						<p>
							This is the flip tool. This tool allows you to flip part of a molecule on the axis of a bond. While this tool is selected, click on a bond and the part of the molecule that is attached to that bond will flip.
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						<a name="clean"></a>
						<img class="inline" src="images/tools-wizard.png"/>
						<p>
							This is the clean tool. By clicking this tool the whole molecule will become "clean." All of the bond angles will fix themselves in an aesthetically pleasing way.
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			<a name="bonds"></a>
			<h2> Bonds </h2>
				<p>
					SME provides you with many types of bonds to connect atoms together with. There are single, double, and triple bonds, as well as wedge and hash bonds. Currently SME does not support cis/trans or hash/wedge bonds. These will be supported in the future.
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				<p>
					In order to add a bond, first click the atom which begins the bond and then either drag the bond to the ending atom, or drag the bond to where you want the ending atom. If you do not connect the bond to an atom, then the currently selected atom type will appear where you release the bond. The type of bond that is added is whatever bond is currently selected in the bond toolbox. If you want to change the bond type, simply select the type of bond you wish to have and click the bond you wish to replace.
				</p>


			<a name="atoms"></a>
			<h2> Atoms </h2>
				<p>
					SME provides you with many different elements to add as atoms.
					In order to add an atom, first select the element which you want to add and then click to position in which you want to add the atom. If you want to change and atom to another element, simply select the element you wish to have and click the atom you wish to replace.
				</p>


			<a name="rings"></a>
			<h2> Rings </h2>
				<p>
					SME provides many different common rings to add to your molecule. In order to add a ring, select it from the items toolbox and then click the position to put the ring.
				</p>


			<a name="files"></a>
			<h1> File Operations </h1>
				<p>
					SME provides you with the ability to save and load files which have molecule structure information. Currently only <i>sdf / molfile</i> is supported.
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			<a name="loading"></a>
			<h2> Loading </h2>
				<p>
					In order to load a file into SME select <i>File</i> &rarr; <i>Load File...</i>. You will be presented with a file dialog. Select the file you want to load and click <i>Open</i>. The current molecule will be replaced with the molecule that you selected to be opened.
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			<a name="saving"></a>
			<h2> Saving </h2>
				<p>
					In order to save a the working molecule to a file select <i>File</i> &rarr; <i>Save File...</i>. You will be presented with a file dialog. Select the file you want to save to and click <i>Save</i>. 
				</p>


			<a name="image"></a>
			<h2> Exporting an Image </h2>
				<p>
					Exporting and image will create an image file out of the current working molecule. In order to export as an image select <i>File</i> &rarr; <i>Export Image...</i>.  You will be presented with a file dialog. Select the file you want to save to and click <i>Save</i>. Currently the only format option is PNG.
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			<a name="inserting"></a>
			<h1> Inserting Fragments </h1>
				<p>
					SME provides you with the ability to insert fragments of molecules by either SMILES string or from the library of fragments included with SME.
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			<a name="library"></a>
			<h2> Molecular Fragment Library </h2>
				<p>
					SME provides a small library of molecular fragments that can be added to a molecule.  Select <i>Insert</i> &rarr; <i>From Library...</i>. A dialog box with a list of molecule names will appear. Select the name of the molecule you wish to add then click <i>OK</i>.
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			<a name="smiles"></a>
			<h2> SMILES Fragments </h2>
				<p>
					SME also provides a method for inserting a fragement (or a whole molecule) by the SMILES string.  Select <i>Insert</i> &rarr; <i>SMILES</i>. A dialog box with a text entry will appear. Type the SMILES string you wish to add then click <i>OK</i>.
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			<a name="view"></a>
			<h1> The View Menu </h1>
				<p>
					The view menu give you options for what you want to see on the screen.
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			<a name="toolboxes"></a>
			<h2> Toolboxes </h2>
				<p>
					You can show and hide the toolboxes (the tools and the items) from the <i>View</i> menu.
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			<a name="hydrogens"></a>
			<h2> Implicit Hydrogens </h2>
				<p>
					The hydrogens in a molecule are hidden by default. If you want to view them in the current molecule select <i> View </i> &rarr; <i> Show Hydrogens</i>. You can also use the same option to hide the hydrogens if they are currently shown.
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			<a name="contribute"></a>
			<h1> Contributing </h1>
				<p>
					Please help us out! Go to <a href="origindb.googlecode.com"> http://origindb.googlecode.com/ </a> or email the developers in the <a href="#contact"> Contact information</a> section for details.
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